With Vince out of the picture because of the "beating" he took from Triple H, Stephanie and Triple H became the new "owners" of the WWE in 2000. This became known as the infamous "McMahon-Helmsley Era". Later in 2000, Stephanie became involved in a love triangle with Triple H and Kurt Angle. This led to many entertaining skits and vignettes. Stephanie and Triple H would eventually be split up after Triple H was sidelined from wrestling in 2001. The two were re-united when Triple H returned in early 2002. The two started having many problems. In hopes of saving the marriage, Steph claimed that she was pregnant. Triple H would go on to divorce Steph after he had found out that she was lieing about the pregnancy the whole time. Stephanie tried to gain redemption by attempting to ruin Triple H's chances of capturing the WWE title. In the process she aligned herself with the undisputed WWE Champion at the time, Chris Jericho. However, Stephanie was unsuccessful as Triple H defeated Jericho to win the title at WM18. A few weeks after Wrestlemania 18, Stephanie competed in a triple threat match involving herself, Chris Jericho, and Triple H. There was a stipulation that if Triple H won the match, Stephanie would be forced to "leave" the WWE. Triple H was victorious which led to Stephanie's very brief sabbatical from WWE TV.

Stephanie made her on-screen return when Vince appointed her as the General Manager of Smackdown on July 18, 2002. She feuded with Eric Bichoff, the General Manager of RAW at the time, for the remainder of 2002. After being credited for the return of Hulk Hogan when she signed him to Smackdown, Stephanie become a face for the first time in 3 years. In mid 2003 Stephanie feuded with Sable, as she did not agree with her sexual relationship with Vince Mcmahon. This led to a match at Vengeance 2003 which Stephanie lost. Vince did not take too kindly to Stephanie's stance on his relationship with Sable, nor did he like many other things about his daughter at the time. Stephanie was eventually "kicked out" of her General Manager position when she lost an "I Quit" match against Vince at No Mercy 2003.

Stephanie returned to WWE TV at WWE Homecoming on October 3, 2005. Beforehand, Austin had stunned both her father Vince and her brother Shane. Stephanie even went as far as slapping Austin which earned her a Stone Cold Stunner as well. Stephanie would also be involved in the firing of Jim Ross 2 weeks later. Stephanie is currently the Senior Vice President of the WWE Creative Team, and the wife of Paul Levesque aka Triple H.